A programmable integrated circuit (IC), such as a field programmable gate array (FPGA), can operate in a variety of modes. One particular mode of operation involves operating multiple transceivers in a programmable IC at different line rates that are not integer multiples of each other. For example, such a mode of operation arises when the programmable IC is used in communication applications in which data is received from multiple sources with different reference frequencies. Generation of clocks for transceivers operating at different line rates typically requires the use of multiple reference oscillators, which increases costs and consumes valuable input/output (IO) resources of the programmable IC. Further, there can be various different requirements for receiving data from the disparate sources at the programmable IC, such as different accuracy requirements.